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Quantifying Three-dimensional Chromatin Organization Utilizing Scanning Transmission Electron Microscopy: ChromSTEM

Yue Li, Eric Roth, Vasundhara Agrawal, Adam Eshein, Jane Fredrick, Luay Almassalha, Anne Shim, Reiner Bleher, Vinayak P. Dravid, Vadim Backman
doi: https://doi.org/10.1101/636209
Yue Li
1Applied Physics Program, Northwestern University, Evanston, Illinois 60208, USA
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Eric Roth
2Department of Materials Sciences and Engineering, Northwestern University, Evanston, Illinois 60208, USA
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Vasundhara Agrawal
3Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
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Adam Eshein
3Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
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Jane Fredrick
3Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
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Luay Almassalha
3Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
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Anne Shim
3Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
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Reiner Bleher
2Department of Materials Sciences and Engineering, Northwestern University, Evanston, Illinois 60208, USA
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Vinayak P. Dravid
2Department of Materials Sciences and Engineering, Northwestern University, Evanston, Illinois 60208, USA
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  • For correspondence: v-backman@northwestern.edu v-dravid@northwestern.edu
Vadim Backman
2Department of Materials Sciences and Engineering, Northwestern University, Evanston, Illinois 60208, USA
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  • For correspondence: v-backman@northwestern.edu v-dravid@northwestern.edu
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Abstract

Chromatin organization over a wide range of length scales plays a critical role in the regulation of gene expression and deciphering these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein we introduce ChromSTEM, a method which utilizes high angle annular dark field imaging and tomography in scanning transmission electron microscopy in combination with DNA-specific staining for electron microscopy. We utilized ChromSTEM to quantify chromatin structure in cultured cells and tissue biopsies through local DNA distribution and the scaling behavior of chromatin polymer. We observed that chromatin is densely packed with an average volume concentration of over 30% with heterochromatin having a two-fold higher density compared to euchromatin. Chromatin was arranged into spatially well-defined nanoscale packing domains with fractal internal structure and genomic size between 100 and 400 kb, comparable to that of topologically associated domains. The packing domains varied in DNA concentration and fractal dimension and had one of the distinct states of chromatin packing with differential ratio of DNA content to the chromatin volume concentration. Finally, we observed a significant intercellular heterogeneity of chromatin organization even within a genetically uniform cell population, which demonstrates the imperative for high-throughput characterization of chromatin structure at the single cell level.

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Posted May 14, 2019.
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Quantifying Three-dimensional Chromatin Organization Utilizing Scanning Transmission Electron Microscopy: ChromSTEM
Yue Li, Eric Roth, Vasundhara Agrawal, Adam Eshein, Jane Fredrick, Luay Almassalha, Anne Shim, Reiner Bleher, Vinayak P. Dravid, Vadim Backman
bioRxiv 636209; doi: https://doi.org/10.1101/636209
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Quantifying Three-dimensional Chromatin Organization Utilizing Scanning Transmission Electron Microscopy: ChromSTEM
Yue Li, Eric Roth, Vasundhara Agrawal, Adam Eshein, Jane Fredrick, Luay Almassalha, Anne Shim, Reiner Bleher, Vinayak P. Dravid, Vadim Backman
bioRxiv 636209; doi: https://doi.org/10.1101/636209

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